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What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention.

Carter CW - Life (Basel) (2015)

Bottom Line: We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code.Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene.Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA. carter@med.unc.edu.

ABSTRACT
We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule.

No MeSH data available.


Urzyme size precludes tRNA anticodon recognition. Urzyme interactions include binding determinants for the tRNA acceptor stem, but cannot interact with the anticodon.
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life-05-00294-f008: Urzyme size precludes tRNA anticodon recognition. Urzyme interactions include binding determinants for the tRNA acceptor stem, but cannot interact with the anticodon.

Mentions: Motivated by our demonstration that aaRS Urzymes cannot interact with the tRNA anticodon (Figure 8) and the proposal [55] that an operational code in the acceptor stem preceded formation of the canonical genetic code, we investigated the unique coding properties of these two regions in tRNAs. We used two bits (pyrimidine vs. purine; number of possible hydrogen bonds in a base pair) to represent the information embedded in each base of the anticodon and acceptor-stem coding regions of tRNAs. This binary coding information for each of the 20 canonical amino acids was used to train regression models for amino acid properties, testing the models against properties of two non-canonical amino acids—selenocysteine and pyrrolysine—outside the training set [56].


What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention.

Carter CW - Life (Basel) (2015)

Urzyme size precludes tRNA anticodon recognition. Urzyme interactions include binding determinants for the tRNA acceptor stem, but cannot interact with the anticodon.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390853&req=5

life-05-00294-f008: Urzyme size precludes tRNA anticodon recognition. Urzyme interactions include binding determinants for the tRNA acceptor stem, but cannot interact with the anticodon.
Mentions: Motivated by our demonstration that aaRS Urzymes cannot interact with the tRNA anticodon (Figure 8) and the proposal [55] that an operational code in the acceptor stem preceded formation of the canonical genetic code, we investigated the unique coding properties of these two regions in tRNAs. We used two bits (pyrimidine vs. purine; number of possible hydrogen bonds in a base pair) to represent the information embedded in each base of the anticodon and acceptor-stem coding regions of tRNAs. This binary coding information for each of the 20 canonical amino acids was used to train regression models for amino acid properties, testing the models against properties of two non-canonical amino acids—selenocysteine and pyrrolysine—outside the training set [56].

Bottom Line: We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code.Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene.Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA. carter@med.unc.edu.

ABSTRACT
We review arguments that biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations, and that the superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code. A coherent structural basis for that scenario was articulated nearly a decade before the demonstration of catalytic RNA. Parallel hierarchical catalytic repertoires for increasingly highly conserved sequences from the two synthetase classes now increase the likelihood that they arose as translation products from opposite strands of a single gene. Sense/antisense coding affords a new bioinformatic metric for phylogenetic relationships much more distant than can be reconstructed from multiple sequence alignments of a single superfamily. Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. That scenario documents a path to increasing complexity that obviates the need for a single polymer to act both catalytically and as an informational molecule.

No MeSH data available.